Citations in PubMed

Primary Citation PubMed: 15610738 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Protein interactions from complexes: a structural perspective.

(2007) Comp Funct Genomics

PubMed: 17538689 | PubMedCentral: PMC1838958 | DOI: 10.1155/2007/49356

Structure Description Chains STP SFP SFN MTP MFP MFN Score spoke Score matrix 1iru 20S proteasome 12 26 40 0 26 40 0 −14 −14 1k8a Large ribosomal subunit 12 0 0 3 5 61 0 −3 &#x... 2212;56 1y1v RNA polymerase II-TFIIs 12 15 32 3 18 48 0 −20 −30 1n32 Small ribosomal subunit 9 1 14 1 3 33 0 −14 −30 1sxj RFC bound to PCNA 5 6 4 0 6 4 0 2 2 1u2v ARP2/3 5 4 2 1 6 4 0 1 2 1id3 Nucleasome 4 2 0 3 5 1 0 −1 4 1gw5 AP2 3 3 0 0 3 0 0 3 3 1kyo Cytochrome BC1 3 1 0 1 2 1 0 0 1 1ntk Cytochrome BC1 3 0 0 1 1 1 0 −1 −1 1qo1 ATP synthase motor 3 1 0 2 3 0 0 −1 3

Publication Year: 2007


Analysis on multi-domain cooperation for predicting protein-protein interactions.

(2007) BMC Bioinformatics 8

PubMed: 17937822 | PubMedCentral: PMC2222654 | DOI: 10.1186/1471-2105-8-391

As an example, Figure 8 illustrates how to reconstruct the RNA Polymerase II-TFIIS complex (PDB ID 1y1v) by our approach at protein, domain and atomic levels respectively with the following five steps...

(a) The RNA Polymerase II-TFIIS complex (PDB ID 1y1v) with 13 subunits (from chain A to chain S).

Publication Year: 2007


GAIA: a gram-based interaction analysis tool--an approach for identifying interacting domains in yeast.

(2009) BMC Bioinformatics 10 Suppl 1

PubMed: 19208164 | PubMedCentral: PMC2648738 | DOI: 10.1186/1471-2105-10-S1-S60

The figure was generated based on the PDB crystal structures (PDB: 1y1v ) using the protein structural viewing tool Cn3D [ 42 ].

Publication Year: 2009


p53 activates transcription by directing structural shifts in Mediator.

(2010) Nat Struct Mol Biol 17

PubMed: 20453859 | PubMedCentral: PMC2932482 | DOI: 10.1038/nsmb.1816

For reference, the structure of the yeast pol II enzyme (pdb 1y1v) is also shown to the same relative scale.

Publication Year: 2010


Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.

(2011) PLoS Biol 9

PubMed: 21468301 | PubMedCentral: PMC3066130 | DOI: 10.1371/journal.pbio.1000603

Because the 12-subunit yeast pol II structure 1Y1V was shown previously to fit well into the human pol II EM structure [29] , the 1Y1V structure was chosen to be displayed.

Pol II Crystal Structure Docking A yeast crystal structure of pol II (PDB 1Y1V) [28] , with the TFIIS fragment removed, was roughly fit into the desired EM structure using Chimera [59] .

The PDB 1Y1V structure is shown throughout the article (with the TFIIS density removed) because this structure was found to correspond most closely to the human pol II cryo-EM structure [29] .

(A) Left: different views (rotation shown at left) of the cryo-EM 3D reconstruction of the Mediator–pol II–TFIIF assembly, rendered to 1.8 MDa; center: the pol II crystal structure (red; PDB 1Y1V) is shown docked within the Mediator–pol II–TFIIF cryo-EM map (blue mesh); right: the pol II crystal structure displayed on its own, with characteristic pol II orientations denoted in red font.

The Mediator–pol II–TFIIF surface is then displayed as blue mesh with a pol II crystal structure (PDB 1Y1V) shown in red ribbon in its docked orientation.

Note the pol II atomic model shown throughout this article is PDB 1Y1V [28] .

The location of pol II within each structure—based upon docking the pol II crystal structure (PDB 1Y1V) in Situs [27] —is denoted by the orange sphere.

Third, identical pol II docking results were calculated from over 20 different pol II crystal structures (e.g. PDB 1Y1V, 1NT9, etc.).

Different views of the free VP16-Mediator structure [19] are shown in purple; pol II is shown in red ribbon (PDB 1Y1V); the Mediator–pol II–TFIIF structure is shown in blue.

Publication Year: 2011


Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo.

(2012) PLoS Genet 8

PubMed: 22511879 | PubMedCentral: PMC3325174 | DOI: 10.1371/journal.pgen.1002627

A. Cartoon representation of “closed” Pol II TL in relation to nucleic acids, Rpb1 bridge helix and a matched GTP substrate from structure PDB 2E2H [1] overlaid with TL constrained in ... pen conformation by TFIIS (not shown) from structure PDB 1Y1V [69] .

Publication Year: 2012


Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage.

(2012) Nucleic Acids Res 40

PubMed: 22396529 | PubMedCentral: PMC3384336 | DOI: 10.1093/nar/gks220

Crosslinking statistics and classification Crosslink pair type Observed pairs Both sites present in PDB 1Y1V Distance ≤30 Å Comment A-A 73 70 68 (97.1%) 2 outliers involve mobile regio... s (bridge helix, clamp) A-B 80 65 39 (60.0%) 22 outliers comprise altered jaw residues a B-B 86 30 13 (43.3%) 13 outliers comprise altered jaw residues a B*-B b 23 b 17 b 2 (11.8%) b 11 outliers comprise altered jaw residues a Total 239 165 120 (72.7%) a The jaw region comprises A190 residues 1252–1487.

Of those, 8 were intra-subunit crosslinks and 19 were crosslinks between A12.2 and other Pol I subunits, which were analyzed with the coordinates of Rpb9 and TFIIS from the Pol II–TFIIS complex structure (PDB 1Y1V) ( 7 ).

Crosslinks were analyzed with the Pol II-TFIIS structure [( 7 ), PDB 1Y1V].

Observed crosslinks are in agreement with the homology model for the Pol I core as judged by analysis with the Pol II X-ray structure (PDB 1Y1V).

Publication Year: 2012


The Mediator complex and transcription regulation.

Crit Rev Biochem Mol Biol 48

PubMed: 24088064 | PubMedCentral: PMC3852498 | DOI: 10.3109/10409238.2013.840259

Pol II is shown in red (PDB 1Y1V).

At center is a “front” view of the Mediator complex, with pol II (red ribbon; PDB 1Y1V) oriented consistent with its bound state orientation in the VP16-Mediator-pol II-TFIIF assembly (Bernecky et al .

Publication Year: null


Transcription bypass of DNA lesions enhances cell survival but attenuates transcription coupled DNA repair.

(2014) Nucleic Acids Res 42

PubMed: 25389266 | PubMedCentral: PMC4245964 | DOI: 10.1093/nar/gku1150

The RNAP II structures are based on PDB 2E2H ( 29 ), which has a closed trigger loop, and PDB 1Y1V ( 30 ), which has an open trigger loop, and generated by using PyMOL.

Publication Year: 2014